Starting phenix.real_space_refine on Mon Nov 17 13:15:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d69_46590/11_2025/9d69_46590.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d69_46590/11_2025/9d69_46590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d69_46590/11_2025/9d69_46590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d69_46590/11_2025/9d69_46590.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d69_46590/11_2025/9d69_46590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d69_46590/11_2025/9d69_46590.map" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.142 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Hg 1 10.96 5 S 22 5.16 5 Na 3 4.78 5 C 2055 2.51 5 N 500 2.21 5 O 562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3143 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3132 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 11, 'TRANS': 400} Chain breaks: 2 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' HG': 1, ' NA': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1577 SG CYS A 269 30.766 23.748 24.903 1.00 69.67 S Time building chain proxies: 1.11, per 1000 atoms: 0.35 Number of scatterers: 3143 At special positions: 0 Unit cell: (59.4, 69.3, 77.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Hg 1 79.96 S 22 16.00 Na 3 11.00 O 562 8.00 N 500 7.00 C 2055 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 136.3 milliseconds 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 1 sheets defined 86.7% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 53 through 82 removed outlier: 3.517A pdb=" N ILE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix removed outlier: 3.734A pdb=" N LEU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 117 removed outlier: 4.257A pdb=" N GLY A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.641A pdb=" N MET A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 211 through 230 removed outlier: 3.832A pdb=" N GLY A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 270 removed outlier: 3.662A pdb=" N TRP A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.601A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 282 through 299 Processing helix chain 'A' and resid 299 through 310 Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.510A pdb=" N MET A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 336 through 348 Processing helix chain 'A' and resid 351 through 363 removed outlier: 3.644A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 367 through 386 Processing helix chain 'A' and resid 390 through 408 removed outlier: 3.861A pdb=" N ILE A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N THR A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 427 removed outlier: 4.337A pdb=" N VAL A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ILE A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 466 removed outlier: 4.002A pdb=" N ILE A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ALA A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N CYS A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LEU A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 475 removed outlier: 4.025A pdb=" N VAL A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 249 hydrogen bonds defined for protein. 744 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.46 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 938 1.34 - 1.45: 359 1.45 - 1.57: 1847 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 3184 Sorted by residual: bond pdb=" N GLN A 413 " pdb=" CA GLN A 413 " ideal model delta sigma weight residual 1.459 1.489 -0.031 1.32e-02 5.74e+03 5.42e+00 bond pdb=" N ARG A 342 " pdb=" CA ARG A 342 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.72e+00 bond pdb=" N ALA A 414 " pdb=" CA ALA A 414 " ideal model delta sigma weight residual 1.459 1.482 -0.024 1.25e-02 6.40e+03 3.60e+00 bond pdb=" C VAL A 411 " pdb=" N PRO A 412 " ideal model delta sigma weight residual 1.332 1.355 -0.023 1.34e-02 5.57e+03 3.00e+00 bond pdb=" C PRO A 412 " pdb=" O PRO A 412 " ideal model delta sigma weight residual 1.233 1.216 0.017 1.19e-02 7.06e+03 2.01e+00 ... (remaining 3179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 4228 1.55 - 3.10: 68 3.10 - 4.64: 20 4.64 - 6.19: 4 6.19 - 7.74: 1 Bond angle restraints: 4321 Sorted by residual: angle pdb=" CA PRO A 412 " pdb=" C PRO A 412 " pdb=" O PRO A 412 " ideal model delta sigma weight residual 121.56 118.09 3.47 1.16e+00 7.43e-01 8.94e+00 angle pdb=" CA ARG A 342 " pdb=" C ARG A 342 " pdb=" O ARG A 342 " ideal model delta sigma weight residual 120.82 118.10 2.72 1.05e+00 9.07e-01 6.72e+00 angle pdb=" CB MET A 255 " pdb=" CG MET A 255 " pdb=" SD MET A 255 " ideal model delta sigma weight residual 112.70 120.44 -7.74 3.00e+00 1.11e-01 6.66e+00 angle pdb=" N ALA A 414 " pdb=" CA ALA A 414 " pdb=" C ALA A 414 " ideal model delta sigma weight residual 111.71 108.77 2.94 1.15e+00 7.56e-01 6.52e+00 angle pdb=" CA MET A 255 " pdb=" CB MET A 255 " pdb=" CG MET A 255 " ideal model delta sigma weight residual 114.10 118.86 -4.76 2.00e+00 2.50e-01 5.66e+00 ... (remaining 4316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 1716 17.66 - 35.32: 127 35.32 - 52.97: 45 52.97 - 70.63: 10 70.63 - 88.29: 6 Dihedral angle restraints: 1904 sinusoidal: 721 harmonic: 1183 Sorted by residual: dihedral pdb=" CB GLU A 345 " pdb=" CG GLU A 345 " pdb=" CD GLU A 345 " pdb=" OE1 GLU A 345 " ideal model delta sinusoidal sigma weight residual 0.00 -88.29 88.29 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU A 469 " pdb=" CG GLU A 469 " pdb=" CD GLU A 469 " pdb=" OE1 GLU A 469 " ideal model delta sinusoidal sigma weight residual 0.00 -87.68 87.68 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB MET A 449 " pdb=" CG MET A 449 " pdb=" SD MET A 449 " pdb=" CE MET A 449 " ideal model delta sinusoidal sigma weight residual 60.00 119.52 -59.52 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 306 0.022 - 0.044: 126 0.044 - 0.067: 73 0.067 - 0.089: 36 0.089 - 0.111: 8 Chirality restraints: 549 Sorted by residual: chirality pdb=" CA VAL A 411 " pdb=" N VAL A 411 " pdb=" C VAL A 411 " pdb=" CB VAL A 411 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.08e-01 chirality pdb=" CA VAL A 203 " pdb=" N VAL A 203 " pdb=" C VAL A 203 " pdb=" CB VAL A 203 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.97e-01 chirality pdb=" CA ILE A 202 " pdb=" N ILE A 202 " pdb=" C ILE A 202 " pdb=" CB ILE A 202 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.73e-01 ... (remaining 546 not shown) Planarity restraints: 527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 445 " 0.256 9.50e-02 1.11e+02 1.15e-01 9.64e+00 pdb=" NE ARG A 445 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 445 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG A 445 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 445 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 342 " 0.259 9.50e-02 1.11e+02 1.16e-01 8.29e+00 pdb=" NE ARG A 342 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 342 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 342 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 342 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 301 " -0.017 5.00e-02 4.00e+02 2.60e-02 1.08e+00 pdb=" N PRO A 302 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 302 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 302 " -0.015 5.00e-02 4.00e+02 ... (remaining 524 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 48 2.66 - 3.22: 3322 3.22 - 3.78: 4828 3.78 - 4.34: 6992 4.34 - 4.90: 11326 Nonbonded interactions: 26516 Sorted by model distance: nonbonded pdb=" O SER A 405 " pdb="NA NA A 602 " model vdw 2.096 2.470 nonbonded pdb=" O THR A 364 " pdb="NA NA A 602 " model vdw 2.101 2.470 nonbonded pdb=" OG1 THR A 102 " pdb="NA NA A 603 " model vdw 2.108 2.470 nonbonded pdb=" OD1 ASP A 368 " pdb="NA NA A 603 " model vdw 2.144 2.470 nonbonded pdb=" OD1 ASN A 366 " pdb="NA NA A 603 " model vdw 2.156 2.470 ... (remaining 26511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.320 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3184 Z= 0.141 Angle : 0.549 7.740 4321 Z= 0.291 Chirality : 0.035 0.111 549 Planarity : 0.008 0.116 527 Dihedral : 15.992 88.291 1140 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 19.48 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.42), residues: 406 helix: 1.02 (0.30), residues: 318 sheet: -1.66 (1.10), residues: 18 loop : -0.87 (0.71), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 445 TYR 0.011 0.001 TYR A 373 PHE 0.013 0.001 PHE A 341 TRP 0.002 0.000 TRP A 19 HIS 0.001 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 3184) covalent geometry : angle 0.54914 ( 4321) hydrogen bonds : bond 0.23834 ( 249) hydrogen bonds : angle 8.47065 ( 744) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.099 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.3550 time to fit residues: 19.6492 Evaluate side-chains 44 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.184050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.135099 restraints weight = 1367.205| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.17 r_work: 0.3382 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3184 Z= 0.161 Angle : 0.560 8.674 4321 Z= 0.296 Chirality : 0.039 0.132 549 Planarity : 0.004 0.025 527 Dihedral : 3.617 12.804 433 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.36 % Allowed : 17.15 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.41), residues: 406 helix: 1.54 (0.28), residues: 325 sheet: -1.48 (1.08), residues: 18 loop : 0.07 (0.82), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 447 TYR 0.013 0.002 TYR A 285 PHE 0.013 0.002 PHE A 341 TRP 0.003 0.001 TRP A 19 HIS 0.001 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 3184) covalent geometry : angle 0.56047 ( 4321) hydrogen bonds : bond 0.04866 ( 249) hydrogen bonds : angle 5.36266 ( 744) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.119 Fit side-chains REVERT: A 252 GLN cc_start: 0.7866 (mt0) cc_final: 0.7655 (mt0) REVERT: A 290 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7573 (mm) REVERT: A 329 MET cc_start: 0.6613 (OUTLIER) cc_final: 0.6136 (mpm) REVERT: A 445 ARG cc_start: 0.7406 (mpt180) cc_final: 0.7030 (mpt-90) REVERT: A 468 LYS cc_start: 0.8061 (ttmt) cc_final: 0.7839 (mttt) outliers start: 15 outliers final: 5 residues processed: 63 average time/residue: 0.4711 time to fit residues: 30.6625 Evaluate side-chains 56 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 364 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.0040 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.186483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.138274 restraints weight = 1426.799| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.19 r_work: 0.3405 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3184 Z= 0.127 Angle : 0.492 5.513 4321 Z= 0.261 Chirality : 0.037 0.129 549 Planarity : 0.003 0.024 527 Dihedral : 3.578 17.182 433 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.36 % Allowed : 16.57 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.41), residues: 406 helix: 1.85 (0.28), residues: 323 sheet: -1.07 (1.10), residues: 18 loop : 0.15 (0.81), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 447 TYR 0.010 0.002 TYR A 285 PHE 0.009 0.001 PHE A 240 TRP 0.002 0.000 TRP A 256 HIS 0.002 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 3184) covalent geometry : angle 0.49211 ( 4321) hydrogen bonds : bond 0.04089 ( 249) hydrogen bonds : angle 4.84759 ( 744) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.123 Fit side-chains REVERT: A 252 GLN cc_start: 0.7725 (mt0) cc_final: 0.7517 (mt0) REVERT: A 290 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7482 (mm) REVERT: A 310 ARG cc_start: 0.7717 (mmt90) cc_final: 0.7133 (tpp80) REVERT: A 342 ARG cc_start: 0.6487 (ttp-110) cc_final: 0.6002 (mtm110) REVERT: A 445 ARG cc_start: 0.7146 (mpt180) cc_final: 0.6710 (mpt-90) outliers start: 15 outliers final: 6 residues processed: 65 average time/residue: 0.4702 time to fit residues: 31.5755 Evaluate side-chains 59 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 364 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.185213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.136148 restraints weight = 1445.855| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.21 r_work: 0.3400 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3184 Z= 0.145 Angle : 0.511 5.928 4321 Z= 0.268 Chirality : 0.038 0.134 549 Planarity : 0.003 0.024 527 Dihedral : 3.610 19.155 433 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.07 % Allowed : 18.90 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.41), residues: 406 helix: 1.80 (0.28), residues: 325 sheet: -1.30 (1.12), residues: 18 loop : -0.03 (0.74), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.010 0.001 TYR A 285 PHE 0.013 0.001 PHE A 240 TRP 0.001 0.000 TRP A 19 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 3184) covalent geometry : angle 0.51062 ( 4321) hydrogen bonds : bond 0.04081 ( 249) hydrogen bonds : angle 4.84723 ( 744) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.089 Fit side-chains REVERT: A 290 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7542 (mm) REVERT: A 297 SER cc_start: 0.8943 (m) cc_final: 0.8730 (p) REVERT: A 310 ARG cc_start: 0.7735 (mmt90) cc_final: 0.7179 (tpp80) REVERT: A 445 ARG cc_start: 0.7293 (mpt180) cc_final: 0.6872 (mpt-90) outliers start: 14 outliers final: 5 residues processed: 64 average time/residue: 0.4313 time to fit residues: 28.6231 Evaluate side-chains 60 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 364 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 12 optimal weight: 0.0010 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.189098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.141015 restraints weight = 1491.915| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.21 r_work: 0.3414 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3184 Z= 0.127 Angle : 0.486 5.224 4321 Z= 0.257 Chirality : 0.038 0.133 549 Planarity : 0.003 0.023 527 Dihedral : 3.549 18.177 433 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.20 % Allowed : 20.35 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.41), residues: 406 helix: 1.91 (0.28), residues: 325 sheet: -1.17 (1.12), residues: 18 loop : -0.07 (0.71), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.010 0.001 TYR A 285 PHE 0.011 0.001 PHE A 240 TRP 0.002 0.000 TRP A 256 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 3184) covalent geometry : angle 0.48625 ( 4321) hydrogen bonds : bond 0.03858 ( 249) hydrogen bonds : angle 4.76410 ( 744) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.120 Fit side-chains REVERT: A 248 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7819 (mmm) REVERT: A 286 MET cc_start: 0.7105 (mtp) cc_final: 0.6811 (mtp) REVERT: A 290 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7563 (mm) REVERT: A 297 SER cc_start: 0.8938 (m) cc_final: 0.8700 (p) REVERT: A 310 ARG cc_start: 0.7738 (mmt90) cc_final: 0.7190 (tpp80) REVERT: A 439 VAL cc_start: 0.7634 (m) cc_final: 0.7431 (p) REVERT: A 445 ARG cc_start: 0.7252 (mpt180) cc_final: 0.6795 (mpt-90) outliers start: 11 outliers final: 5 residues processed: 61 average time/residue: 0.4375 time to fit residues: 27.6622 Evaluate side-chains 60 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 364 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.0970 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 25 optimal weight: 0.0770 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.194232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.147092 restraints weight = 1513.832| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.23 r_work: 0.3449 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3184 Z= 0.115 Angle : 0.468 5.136 4321 Z= 0.249 Chirality : 0.038 0.132 549 Planarity : 0.003 0.023 527 Dihedral : 3.490 17.568 433 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.62 % Allowed : 22.09 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.41), residues: 406 helix: 2.05 (0.28), residues: 326 sheet: -0.95 (1.13), residues: 18 loop : 0.10 (0.72), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.009 0.001 TYR A 285 PHE 0.009 0.001 PHE A 218 TRP 0.001 0.000 TRP A 256 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 3184) covalent geometry : angle 0.46831 ( 4321) hydrogen bonds : bond 0.03612 ( 249) hydrogen bonds : angle 4.64670 ( 744) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.117 Fit side-chains REVERT: A 138 THR cc_start: 0.7156 (OUTLIER) cc_final: 0.6785 (p) REVERT: A 248 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7708 (mmm) REVERT: A 290 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7625 (mm) REVERT: A 297 SER cc_start: 0.8940 (m) cc_final: 0.8693 (p) REVERT: A 310 ARG cc_start: 0.7755 (mmt90) cc_final: 0.7209 (tpp80) REVERT: A 445 ARG cc_start: 0.7216 (mpt180) cc_final: 0.6737 (mpt-90) outliers start: 9 outliers final: 3 residues processed: 60 average time/residue: 0.4191 time to fit residues: 26.0561 Evaluate side-chains 58 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.0070 chunk 2 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 36 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.191111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.143121 restraints weight = 1577.090| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.25 r_work: 0.3456 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3184 Z= 0.121 Angle : 0.483 5.155 4321 Z= 0.254 Chirality : 0.038 0.134 549 Planarity : 0.003 0.023 527 Dihedral : 3.487 18.521 433 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.91 % Allowed : 22.97 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.41), residues: 406 helix: 2.05 (0.28), residues: 326 sheet: -0.89 (1.11), residues: 18 loop : -0.00 (0.71), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.009 0.001 TYR A 285 PHE 0.010 0.001 PHE A 240 TRP 0.001 0.000 TRP A 19 HIS 0.001 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 3184) covalent geometry : angle 0.48308 ( 4321) hydrogen bonds : bond 0.03629 ( 249) hydrogen bonds : angle 4.66412 ( 744) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.126 Fit side-chains REVERT: A 138 THR cc_start: 0.7130 (OUTLIER) cc_final: 0.6788 (p) REVERT: A 248 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7736 (mmm) REVERT: A 290 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7608 (mm) REVERT: A 310 ARG cc_start: 0.7754 (mmt90) cc_final: 0.7238 (tpp80) REVERT: A 445 ARG cc_start: 0.7231 (mpt180) cc_final: 0.6746 (mpt-90) outliers start: 10 outliers final: 4 residues processed: 63 average time/residue: 0.4463 time to fit residues: 29.1059 Evaluate side-chains 62 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 343 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 17 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.188988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.140230 restraints weight = 1618.515| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.27 r_work: 0.3427 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3184 Z= 0.129 Angle : 0.499 5.201 4321 Z= 0.260 Chirality : 0.038 0.131 549 Planarity : 0.003 0.023 527 Dihedral : 3.507 19.680 433 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.91 % Allowed : 23.55 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.41), residues: 406 helix: 1.97 (0.28), residues: 326 sheet: -0.93 (1.11), residues: 18 loop : -0.41 (0.68), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.009 0.001 TYR A 285 PHE 0.017 0.001 PHE A 341 TRP 0.002 0.000 TRP A 256 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 3184) covalent geometry : angle 0.49945 ( 4321) hydrogen bonds : bond 0.03695 ( 249) hydrogen bonds : angle 4.68644 ( 744) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.109 Fit side-chains REVERT: A 138 THR cc_start: 0.7202 (OUTLIER) cc_final: 0.6868 (p) REVERT: A 248 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7719 (mmm) REVERT: A 252 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7610 (mm-40) REVERT: A 290 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7631 (mm) REVERT: A 310 ARG cc_start: 0.7763 (mmt90) cc_final: 0.7253 (tpp80) REVERT: A 445 ARG cc_start: 0.7260 (mpt180) cc_final: 0.6801 (mpt-90) outliers start: 10 outliers final: 4 residues processed: 67 average time/residue: 0.4649 time to fit residues: 32.1948 Evaluate side-chains 66 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 343 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.190619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.143503 restraints weight = 1620.583| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.19 r_work: 0.3420 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3184 Z= 0.156 Angle : 0.549 6.128 4321 Z= 0.281 Chirality : 0.040 0.138 549 Planarity : 0.004 0.027 527 Dihedral : 3.618 22.135 433 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.78 % Allowed : 23.55 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.41), residues: 406 helix: 1.86 (0.28), residues: 325 sheet: -1.05 (1.09), residues: 18 loop : -0.24 (0.71), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 61 TYR 0.008 0.001 TYR A 285 PHE 0.016 0.002 PHE A 240 TRP 0.001 0.000 TRP A 256 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 3184) covalent geometry : angle 0.54885 ( 4321) hydrogen bonds : bond 0.03955 ( 249) hydrogen bonds : angle 4.79107 ( 744) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.075 Fit side-chains REVERT: A 138 THR cc_start: 0.7201 (OUTLIER) cc_final: 0.6859 (p) REVERT: A 248 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7576 (mmm) REVERT: A 252 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7351 (mm-40) REVERT: A 290 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7293 (mm) REVERT: A 310 ARG cc_start: 0.7633 (mmt90) cc_final: 0.7070 (tpp80) REVERT: A 445 ARG cc_start: 0.7042 (mpt180) cc_final: 0.6580 (mpt-90) outliers start: 13 outliers final: 6 residues processed: 64 average time/residue: 0.4381 time to fit residues: 28.9954 Evaluate side-chains 65 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 365 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.195809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.148958 restraints weight = 1630.589| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.23 r_work: 0.3448 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3184 Z= 0.137 Angle : 0.536 6.654 4321 Z= 0.277 Chirality : 0.039 0.137 549 Planarity : 0.003 0.025 527 Dihedral : 3.607 21.142 433 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.49 % Allowed : 23.55 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.41), residues: 406 helix: 1.81 (0.28), residues: 325 sheet: -0.97 (1.11), residues: 18 loop : -0.21 (0.72), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.009 0.001 TYR A 285 PHE 0.012 0.001 PHE A 240 TRP 0.003 0.000 TRP A 256 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 3184) covalent geometry : angle 0.53587 ( 4321) hydrogen bonds : bond 0.03812 ( 249) hydrogen bonds : angle 4.77029 ( 744) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.129 Fit side-chains REVERT: A 138 THR cc_start: 0.7300 (OUTLIER) cc_final: 0.6938 (p) REVERT: A 248 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7736 (mmm) REVERT: A 252 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7510 (mm-40) REVERT: A 290 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7633 (mm) REVERT: A 310 ARG cc_start: 0.7751 (mmt90) cc_final: 0.7232 (tpp80) REVERT: A 445 ARG cc_start: 0.7190 (mpt180) cc_final: 0.6724 (mpt-90) outliers start: 12 outliers final: 6 residues processed: 64 average time/residue: 0.4377 time to fit residues: 28.9774 Evaluate side-chains 64 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 343 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.189300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.141128 restraints weight = 1701.090| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.25 r_work: 0.3469 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3184 Z= 0.145 Angle : 0.547 6.468 4321 Z= 0.285 Chirality : 0.039 0.155 549 Planarity : 0.003 0.026 527 Dihedral : 3.647 21.530 433 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.91 % Allowed : 24.42 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.41), residues: 406 helix: 1.77 (0.28), residues: 325 sheet: -0.96 (1.11), residues: 18 loop : -0.28 (0.71), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.009 0.001 TYR A 285 PHE 0.014 0.002 PHE A 240 TRP 0.007 0.001 TRP A 276 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 3184) covalent geometry : angle 0.54722 ( 4321) hydrogen bonds : bond 0.03865 ( 249) hydrogen bonds : angle 4.81048 ( 744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1430.27 seconds wall clock time: 25 minutes 10.29 seconds (1510.29 seconds total)